Comparison between the types for the genders (after controlling for age)

Questions

  • What are the differences between the types for the genders?
  • Do we observe the same changes as globally?

Loads

Libraries and functions

==========================================================================
*
*  Package WGCNA 1.63 loaded.
*
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R. 
*    To allow multi-threading within WGCNA with all available cores, use 
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example 
*
*          ALLOW_WGCNA_THREADS=4
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=4
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================


Allowing multi-threading with up to 4 threads.

preparing gene to GO mapping data...
preparing IC data...
preparing gene to GO mapping data...
preparing IC data...
preparing gene to GO mapping data...
preparing IC data...

Data

Stats

Wald padj < 0.05LFC > 0 (Wald padj < 0.05)LFC < 0 (Wald padj < 0.05)
GF VS SPF (F)8.093.314.78
GF VS SPF (M)4.561.842.71

Differentially expressed genes

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”

Counts

GF != SPF for F with abs(FC) > 2

GF != SPF for M with abs(FC) > 2

Comparison of the numbers per types

Differentially expressed genes

DEG into gene co-expression network

  • White: up-regulated
  • Black: down-regulated

Female

Male

Global

GO analysis

Biological process

Dot-plot with the most over-represented BP GO (20 most significant p-values for the different comparison)

Network based on description similarity

52w VS 8w

F

scatterplotThree

M

scatterplotThree

Global

scatterplotThree

Cellular components

Dot-plot with the most over-represented CC GO (20 most significant p-values for the different comparison)

Warning message:
“Removed 3 rows containing missing values (geom_point).”

Molecular functions

Dot-plot with the most over-represented MF GO (20 most significant p-values for the different comparison)

Warning message:
“Removed 3 rows containing missing values (geom_point).”

KEGG pathways

[1] "Note: 8 of 2920 unique input IDs unmapped."

[1] "Note: 8 of 2920 unique input IDs unmapped."

Warning message in file.rename(from = paste("mmu", cat, ".pathview.multi.png", sep = ""), :
“cannot rename file 'mmu00514.pathview.multi.png' to '../results/dge/type-effect/type_gender/under_repr_kegg/mmu00514.pathview.multi.png', reason 'No such file or directory'”